git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118094 bc3139a8-67e5-0310-9ffc-ced21a209358
g.yu authored on 02/06/2016 03:29:16
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.5 |
| 2 | 2 |
------------------------ |
| 3 |
+ o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu> |
|
| 3 | 4 |
o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu> |
| 4 | 5 |
+ as.Date won't work for BCE time. |
| 5 | 6 |
+ as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object). |
| ... | ... |
@@ -60,7 +60,7 @@ collapse <- function(tree_view=NULL, node) {
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| 60 | 60 |
sp <- get.offspring.df(df, node) |
| 61 | 61 |
sp.df <- df[sp,] |
| 62 | 62 |
df[node, "isTip"] <- TRUE |
| 63 |
- sp_y <- range(sp.df$y) |
|
| 63 |
+ sp_y <- range(sp.df$y, na.rm=TRUE) |
|
| 64 | 64 |
ii <- which(df$y > max(sp_y)) |
| 65 | 65 |
if (length(ii)) {
|
| 66 | 66 |
df$y[ii] <- df$y[ii] - diff(sp_y) |